Author: rodche
Date: 2012-03-27 10:05:51 -0700 (Tue, 27 Mar 2012)
New Revision: 28666
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
Log:
minor change
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
2012-03-27 16:43:42 UTC (rev 28665)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
2012-03-27 17:05:51 UTC (rev 28666)
@@ -4,15 +4,16 @@
import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskIterator;
-public class BioPaxReaderTaskFactory extends SimpleInputStreamTaskFactory {
+public class BioPaxReaderTaskFactory implements InputStreamTaskFactory<Object>
{
+ private final CyFileFilter filter;
private final CyNetworkFactory networkFactory;
private final CyNetworkViewFactory viewFactory;
private final CyNetworkNaming naming;
@@ -23,7 +24,7 @@
public BioPaxReaderTaskFactory(CyFileFilter filter, CyNetworkFactory
networkFactory,
CyNetworkViewFactory viewFactory, CyNetworkNaming
naming,
VisualMappingManager mappingManager,
BioPaxVisualStyleUtil bioPaxVisualStyleUtil) {
- super(filter);
+ this.filter = filter;
this.networkFactory = networkFactory;
this.viewFactory = viewFactory;
this.naming = naming;
@@ -31,16 +32,34 @@
this.bioPaxVisualStyleUtil = bioPaxVisualStyleUtil;
}
+
@Override
- public TaskIterator createTaskIterator(InputStream inputStream, String
inputName) {
- if (inputName == null) {
+ public CyFileFilter getFileFilter() {
+ return filter;
+ }
+
+
+ @Override
+ public TaskIterator createTaskIterator(Object tunableContext,
+ InputStream is, String inputName) {
+ if(inputName == null)
inputName = "BioPAX_Network"; //default name fallback
- }
-
+
BioPaxReaderTask task = new BioPaxReaderTask(
- inputStream, inputName, networkFactory,
viewFactory, naming,
+ is, inputName, networkFactory, viewFactory,
naming,
mappingManager, bioPaxVisualStyleUtil);
return new TaskIterator(task);
}
+ @Override
+ public boolean isReady(Object tunableContext, InputStream is,
+ String inputName) {
+ return true;
+ }
+
+ @Override
+ public Object createTunableContext() {
+ return null;
+ }
+
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-03-27 16:43:42 UTC (rev 28665)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-03-27 17:05:51 UTC (rev 28666)
@@ -70,9 +70,9 @@
BioPaxVisualStyleUtil bioPaxVisualStyleUtil = new
BioPaxVisualStyleUtil(visualStyleFactoryRef,visualMappingManagerRef,discreteMappingFunctionFactoryRef,passthroughMappingFunctionFactoryRef);
BioPaxViewTracker bioPaxViewTracker = new
BioPaxViewTracker(bioPaxDetailsPanel,bioPaxContainer, cyApplicationManagerRef,
visualMappingManagerRef, bioPaxVisualStyleUtil);
- InputStreamTaskFactory inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,visualMappingManagerRef,bioPaxVisualStyleUtil);
+ InputStreamTaskFactory<?> inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,visualMappingManagerRef,bioPaxVisualStyleUtil);
CytoPanelComponent cytoPanelComponent = new
BioPaxCytoPanelComponent(bioPaxContainer);
- ExportAsBioPAXAction exportAsBioPAXAction = new
ExportAsBioPAXAction(fileUtilRef, cyApplicationManagerRef, bioPaxFilter,
taskManagerRef);
+// ExportAsBioPAXAction exportAsBioPAXAction = new
ExportAsBioPAXAction(fileUtilRef, cyApplicationManagerRef, bioPaxFilter,
taskManagerRef);
// register/export core Cytoscape osgi service implementations
registerService(bc,inputStreamTaskFactory,InputStreamTaskFactory.class, new
Properties());
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